Cant help with the second question.
But you can get Onyx coins in Arcade and Puzzle Kombat too.
To get more, set it to hard or max difficulty. You will get like double the normal.

I'll try setting it to hard. I've played a lot of Arcade matches on Medium and I haven't received a single Onyx Koin that way, same with Puzzle. Thanx for the answer!...
...I guess I'll wait and see if someone can help me with the second one.

In earthrealm where you knock out the old man ( the kid should still be there calling u a murderer). Look inbetween the tree, and the hut farthest to your left, and youll see motaro he'll give you 1000 onyx. Youll have to meditate for a day to get the time down. i believe it may be around 10 am.
And also meat in netherealm gives 1000 onyx i think.
Go all the way to the right after you leave the town then hug the wall tell you see a cave with a skeleton in it, and meditate. Other then that arcade on hards probably your best bet.
As for the quests you missed, so did i so cant help ya there.. i dont know of any way to get them after you beat konquest.

Well thanks!!...Meat does give you 1000 Onyx!!. However, Motaro gave me 1000 Ruby instead of Onyx...heh.